Evan W. Carson

In the San Francisco Estuary, non‐native Wakasagi Hypomesus nipponensis hybridize with endemic and endangered Delta Smelt H. transpacificus , and all wild‐caught hybrids have a maternal Wakasagi parent. However, the mechanisms that facilitate or impede hybridization and explain sex‐biased hybrid asymmetry between these two species remain unclear. We conducted a no‐choice spawning experiment, in which wild‐caught Wakasagi (WK) and cultured Delta Smelt (DS) spawned naturally in different species‐sex combinations: five Delta Smelt females with five Wakasagi males (DS × WK), five Wakasagi females with five Delta Smelt males (WK × DS) and five Wakasagi females with five Wakasagi males (WK × WK). We compared these data to those from a previous study testing DS × DS using the same methods. We quantified the frequency of spawns and attempts, sex ratio of participants and diel timing of behaviours, as well as the fertilization success of resulting eggs. Wakasagi engaged in five times more spawns than Delta Smelt in same‐species trials, and spawns were more frequent in WK × DS than in DS × WK trials. Whereas fish in WK × WK trials exhibited mostly diurnal spawns, those in all other crosses exhibited predominantly nocturnal spawns. Eggs resulting from WK × DS trials had lower fertilization success than those in all other crosses. These results did not clearly explain the hybrid asymmetry observed in nature. Nevertheless, our study demonstrated that: 1) Wakasagi exhibited a very high propensity to spawn, which may provide a reproductive advantage over Delta Smelt, 2) Wakasagi showed great plasticity in spawning behaviour, which may facilitate interspecific spawning and 3) all crosses produced fertilized eggs, demonstrating that there are no complete pre‐zygotic barriers to hybridization. Ultimately, any level of Delta Smelt spawning activity that includes Wakasagi is wasted reproductive potential, and our study highlights the mechanisms by and degree to which this may occur.

Effective population size ( N _e ), census size ( N _c ) and their ratio ( N _e / N _c ) are widely used indicators in conservation genetics, yet long‐term empirical data tracking of all three metrics over long time scales in wild populations remains rare. Using monitoring data from 1995 to 2020, we examined temporal dynamics of N _e , N _c and their relationship during the demographic collapse of Delta Smelt ( Hypomesus transpacificus ), an endangered fish endemic to the San Francisco Estuary, California, USA. We estimated N _e for 21 annual cohorts using restriction site‐associated DNA sequencing data, applying the linkage disequilibrium method, temporal method and a recently developed combined method. Abundance was represented by model‐based survey indices ( N _c *). N _e varied substantially through time (145–1928), declining in recent years but remaining above commonly cited conservation thresholds for long‐term persistence (e.g., N _e > 500) until the final years of collapse. N _e was positively correlated with N _c * ( r = 0.58), but the shallow slope (β = 0.25) indicates that demographic decline outpaced genetic decline. N _e / N _c * was consistently low (0.0001–0.056), but it increased significantly through time. Our results show that genetic erosion may lag behind demographic collapse and that N _e / N _c * is not constant and therefore cannot be easily inferred from either variable alone. This study demonstrates the need for additional empirical data sets to facilitate interpretation of N _e , N _c * and N _e / N _c * for the conservation of global biodiversity.

Objective: Delta Smelt Hypomesus transpacificus are thought to be close to extinction in the wild, which has spurred multiagency conservation efforts to supplement their population. In conjunction with these recent efforts, monitoring is needed to assess the effectiveness of supplementation. Such monitoring often uses large-scale tagging of released fish to distinguish between hatchery-origin and wild-origin fish that are captured during later surveys. Methods: In this study, we evaluated the use of visible implant elastomer tags in Delta Smelt to determine whether fish survival, fish growth, or tag retention were dependent on (1) tag color (blue, green, orange, red, yellow, and no-tag control) or (2) tagged body location (posterior-dorsal, anterior-dorsal, mid-lateral line, and no-tag control). Result: Over 165 days of the first experiment, there was no difference in growth rate (mean = 0.073 mm/d, range = 0.072–0.075 mm/d) or survival (mean = 68%, range = 63–77%) among tag colors. Across all color groups, mean tag retention was 96% (range = 87–100%). Over 120 days of the second experiment, tag location had no influence on fish growth rate (mean = 0.064 mm/d, range = 0.062–0.067 mm/d) or survival (mean = 50%, range = 43–58%). For the surviving fish in experiment 2, the tags that were placed at the mid-lateral line were retained less (84% on day 120) than those at posterior-dorsal and anterior-dorsal locations (99% and 98%, respectively). Conclusion: Our results suggest that visible implant elastomer tagging is a suitable method for marking adult Delta Smelt (>50 mm fork length) for up to 165 days and can be useful for conservation monitoring efforts.

Adaptation to captivity in spawning programs can lead to unintentional consequences, such as domestication that results in reduced fitness in the wild. The timing of sexual maturation has been shown to be a trait under domestication selection in fish hatcheries, which affects a fish's access to mating opportunities and aligning their offspring's development with favorable environmental conditions. Earlier maturing fish may be favored in hatchery settings where managers provide artificially optimal growing conditions, but early maturation may reduce fitness in the wild if, for example, there is a mismatch between timing of reproduction and availability of resources that support recruitment. We investigated patterns of maturation timing in a delta smelt (Hypomesus transpacificus) conservation hatchery by quantifying changes to the median age at maturity since the captive spawning program was initiated in 2008. Over the span of a decade, we observed a small, but significant increase in age at maturity among broodstock by 2.2 weeks. This trait had low heritability and was largely controlled by phenotypic plasticity that was dependent on the time of year fish were born. Fish that were born later in the year matured faster, potentially a carryover from selection favoring synchronous spawning in the wild. However, higher DI (domestication index) fish showed a loss of plasticity, we argue, as a result of hatchery practices that breed individuals past peak periods of female ripeness. Our findings suggest that the hatchery setting has relaxed selection pressures for fish to mature quickly at the end of the year and, consequently, has led to a loss of plasticity in age at maturity. Hatchery fish that are re‐introduced in the wild may not be able to align maturation with population peaks if their maturation rates are too slow with reduced plasticity, potentially resulting in lower fitness.

Objective: A small-scale culture system effective in producing larvae of endangered Delta Smelt Hypomesus transpacificus was recently developed to facilitate conservation and research efforts. Methods: To optimize its use, we examined the effect of stocking density (300, 500, 700, and 900 fish per 92 L of water) on the length, weight, and survival of late-stage larvae (41 days posthatch) reared for 40 days in the small-scale system. Result: Stocking density had no effect on larval survival or size. Also, the survival, length, and weight of these fish did not differ from those reared using standard, large-scale culture practices (2500 fish per 320 L of water). Conclusion: Our findings validate the methods used for small-scale Delta Smelt rearing, help optimize these protocols, and thereby enhance Delta Smelt rearing capabilities needed for research and conservation.

Objective: To support the declining wild population of Delta Smelt, a conservation hatchery has expanded its mission from maintaining a backup population as insurance against extinction to also producing fish for release into the wild. The substantially higher production demands require a balance between producing large numbers of fish while adhering to conservation genetic principles that maximize retention of effective population size (Ne) and thus overall diversity. Methods: We performed spawning experiments at the hatchery to evaluate the genetic consequences of two spawning strategies: (1) a pooled strategy where we fertilized premixed eggs from three dams with premixed milt from three sires and (2) a partial-factorial strategy where eggs from three dams were mixed and then apportioned among three containers, each container then receiving milt from one sire. We used genetic parentage analysis of larval offspring to determine the reproductive success of spawners in 10 replicate crosses of each strategy. Result: The contributions of parents to offspring were more even in partial-factorial crosses and consequently resulted in higher Ne (average Ne = 5.50 ± 0.38; expected Ne = 6.0), suggesting its potential for maintaining genetic diversity over time. In contrast, our pooled spawning experiment produced lower and more variable Ne values (average Ne = 3.86 ± 1.30), demonstrating that this more efficient method of production entails high costs in terms of long-term genetic management. Treating our experiments as hypothetical pools of fish for release, we combined the Ne values for pooled or partial-factorial crosses to calculate the effective size of a release population (NeR). Unequal family sizes reduced NeR for our pooled experiment to half of the expected value, whereas the partial-factorial experiment NeR was 88% of the expected value. Conclusion: We discuss the benefits and risks of each method and how these can be considered when designing a spawning strategy for Delta Smelt supplementation.

Since 2008, a refuge population of Delta Smelt Hypomesus transpacificus has been cultured in a conservation hatchery to help protect the imperiled species from extinction. Culture techniques for this population have thus far focused on maximizing genetic diversity in conjunction with large-scale operations (40 larval tanks, 5,954-L larval system, 224,000 larvae capacity), which includes rearing multiple family groups within the same tanks. However, Delta Smelt production and associated research projects would benefit from also being able to rear fish on a smaller scale, such as in individual family groups. Recently, a new culture system and modified culture practices were developed for rearing small groups of larval Delta Smelt. We (1) determined the performance of the small-scale “experimental” rearing system from embryo to 80 d posthatch (dph) and (2) tested whether the performance of the experimental system met the standard set by the large-scale “refuge” rearing system at critical culturing life stages in terms of embryo hatching rate (10 d postfertilization) and larval survival, length, and weight (40 and 80 dph). From 1,000 embryos, the experimental system produced a mean ± SE of 376 ± 44 late-stage larvae. The hatching rate of embryos did not differ between systems. Early-stage larvae (0–40 dph) reared in the experimental system did not differ in survival rate but were longer and heavier than those reared in the refuge system. In contrast, late-stage larvae (41–80 dph) reared in the experimental system had poorer survival and were shorter and lighter than refuge-reared larvae. Thus, the experimental system met the refuge-system benchmark for embryo hatching and exceeded the benchmark in early-larval production, but it could be improved for late-larval rearing. Nevertheless, this small-scale rearing system will provide much-needed flexibility to enhance Delta Smelt culture practices and facilitate future research.